Use the vertical space!! And make the Gas Giants have a bigger grav well too. Obviously, they should have bigger planet sizes. I also thing the normal planets should have a bigger well then asteroids.
If by using vertical space you are talking about making it in true 3d, I think that that would get really messy pretty quickly.
Normal Planets do have a larger gravity well than asteroids. You can tell this when putting down a repair station, it covers nearly the entire asteroid well, but only about a third of a planetary well. The Sun's grav wells are much larger than both of them.
On the original suggestions of the thread:
1. The entire system is rotating very slowly silly, all fused together, the reason that you don't notice is that the devs made the camera rotate at the same rate so that it wouldn't be disorienting! Really though, having rotating planets is a neat idea, but if they all rotate at the same rate it will look like the devs couldn't handle the complexities of true rotation in a way that they thought added to the game, so they just added in a lame cop out that was equally unrealistic for.... no real reason. And that's exactly what it would be.
2. I think that the idea of colonizable moons is a neat one which deserves a closer look. As for other space junk, there is already minable asteroids, smaller asteroids in asteroid systems, debris left from destroyed stations and cap ships, so it seems like it's pretty much covered. Yes you can move through them, but I think the fact that fighters move through even planets (and suns) shows that the collision avoidance work simply hasn't been done yet.
3. I agree that a little bit more motion in the space battles would be nice, although you could have phrased it (as with everything else) much more tactfully.
4. I have no idea what you are talking about with this gravity ring, I was thinking it was the traffic between space elevators, but that would be in a lower planetary orbit and there would hardly be any atmosphere, and even if there was some (like in ours, a very tiny amount) it wouldn't affect orbit speed. The idea of certain areas having little quirks like slower shield regeneration, as well as your reasoning for it, is quite interesting, and I think that that's the sort of thing that could turn out really well if it was used here or there.
5. More planetary types would be nice
6. I like most of the ship models (especially the Akkan, although perhaps its military features could be made a little more prominent, but this is going to be a matter of taste that will vary for many people. It's also a matter of taste on the part of the TEC. It's not a military oriented race, so it makes sense that guns and things seem a little tacked on.